Multiple sequence alignment - TraesCS4B01G297600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G297600 chr4B 100.000 3432 0 0 1 3432 582920576 582917145 0.000000e+00 6338
1 TraesCS4B01G297600 chr4B 97.647 85 2 0 3348 3432 303692283 303692367 2.760000e-31 147
2 TraesCS4B01G297600 chr4B 94.382 89 5 0 3344 3432 648415942 648416030 1.660000e-28 137
3 TraesCS4B01G297600 chr4A 90.813 2362 140 26 446 2766 4641806 4644131 0.000000e+00 3088
4 TraesCS4B01G297600 chr4A 91.461 445 28 5 8 443 4641325 4641768 1.360000e-168 603
5 TraesCS4B01G297600 chr4D 89.808 2443 179 32 841 3261 465900315 465897921 0.000000e+00 3068
6 TraesCS4B01G297600 chr4D 92.287 376 19 6 1 373 465907709 465907341 3.030000e-145 525
7 TraesCS4B01G297600 chr7D 85.789 1140 124 21 525 1652 104187836 104188949 0.000000e+00 1173
8 TraesCS4B01G297600 chr7D 85.237 1138 141 11 522 1654 104210419 104211534 0.000000e+00 1146
9 TraesCS4B01G297600 chr7D 84.703 438 65 2 1973 2409 104211607 104212043 1.460000e-118 436
10 TraesCS4B01G297600 chr7D 96.471 85 3 0 3262 3346 99687659 99687743 1.280000e-29 141
11 TraesCS4B01G297600 chr7D 95.349 86 4 0 3261 3346 478405733 478405818 1.660000e-28 137
12 TraesCS4B01G297600 chr7D 95.294 85 4 0 3262 3346 488888557 488888473 5.970000e-28 135
13 TraesCS4B01G297600 chr7D 91.753 97 7 1 3250 3346 499413041 499412946 2.150000e-27 134
14 TraesCS4B01G297600 chr7B 85.501 1138 135 13 525 1654 62466073 62467188 0.000000e+00 1160
15 TraesCS4B01G297600 chr7B 96.629 89 2 1 3344 3431 658176440 658176528 2.760000e-31 147
16 TraesCS4B01G297600 chr7B 96.429 84 3 0 3349 3432 7319892 7319975 4.620000e-29 139
17 TraesCS4B01G297600 chr7B 95.402 87 4 0 3346 3432 281309245 281309331 4.620000e-29 139
18 TraesCS4B01G297600 chr3B 98.837 86 1 0 3347 3432 658356534 658356449 1.650000e-33 154
19 TraesCS4B01G297600 chr3B 95.349 86 4 0 3261 3346 565053841 565053926 1.660000e-28 137
20 TraesCS4B01G297600 chr1B 98.837 86 1 0 3347 3432 607481798 607481883 1.650000e-33 154
21 TraesCS4B01G297600 chr2A 97.674 86 2 0 3261 3346 399013345 399013430 7.670000e-32 148
22 TraesCS4B01G297600 chr2A 95.349 86 4 0 3261 3346 398306285 398306200 1.660000e-28 137
23 TraesCS4B01G297600 chr5B 95.402 87 4 0 3346 3432 295484946 295484860 4.620000e-29 139
24 TraesCS4B01G297600 chr3D 95.402 87 4 0 3346 3432 607699547 607699461 4.620000e-29 139
25 TraesCS4B01G297600 chr3D 95.294 85 4 0 3262 3346 499436088 499436004 5.970000e-28 135
26 TraesCS4B01G297600 chr3A 95.349 86 4 0 3261 3346 330189513 330189428 1.660000e-28 137
27 TraesCS4B01G297600 chr7A 77.404 208 47 0 1425 1632 19151851 19151644 1.290000e-24 124


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G297600 chr4B 582917145 582920576 3431 True 6338.0 6338 100.000 1 3432 1 chr4B.!!$R1 3431
1 TraesCS4B01G297600 chr4A 4641325 4644131 2806 False 1845.5 3088 91.137 8 2766 2 chr4A.!!$F1 2758
2 TraesCS4B01G297600 chr4D 465897921 465900315 2394 True 3068.0 3068 89.808 841 3261 1 chr4D.!!$R1 2420
3 TraesCS4B01G297600 chr7D 104187836 104188949 1113 False 1173.0 1173 85.789 525 1652 1 chr7D.!!$F2 1127
4 TraesCS4B01G297600 chr7D 104210419 104212043 1624 False 791.0 1146 84.970 522 2409 2 chr7D.!!$F4 1887
5 TraesCS4B01G297600 chr7B 62466073 62467188 1115 False 1160.0 1160 85.501 525 1654 1 chr7B.!!$F2 1129

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
253 262 0.798776 AAGACGATGGCTTGCTTTCG 59.201 50.000 13.09 13.09 37.60 3.46 F
1183 1250 1.282875 GAACGGTGGAACAAGCTGC 59.717 57.895 0.00 0.00 44.16 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1534 0.033090 GGACGTTCTCCTGGACGTTT 59.967 55.0 12.5 0.0 39.02 3.60 R
2730 2856 0.035725 GGTAAAGGAGGGTTGTCGGG 60.036 60.0 0.0 0.0 0.00 5.14 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 7.275123 TGTTTTTAACCGATTTTAAGCAAACGT 59.725 29.630 0.00 0.00 30.75 3.99
44 45 3.312973 ACCGATTTTAAGCAAACGTGTGA 59.687 39.130 10.72 0.00 0.00 3.58
49 50 6.575572 CGATTTTAAGCAAACGTGTGACATAA 59.424 34.615 10.72 2.19 0.00 1.90
70 71 3.684103 TTTTCGAACACGACATTTGCT 57.316 38.095 0.00 0.00 35.76 3.91
115 122 7.873739 AAAACAACACTAAATCATAGCTTGC 57.126 32.000 0.00 0.00 0.00 4.01
142 149 7.438160 TCTTCATTCTAACGTTACCATAGCATG 59.562 37.037 3.29 2.77 0.00 4.06
167 174 2.355197 TCCGTAAGATGCCAACATGTG 58.645 47.619 0.00 0.00 36.35 3.21
190 199 1.813513 CAAGTCGAGGTGGCATTCTT 58.186 50.000 0.00 0.00 0.00 2.52
253 262 0.798776 AAGACGATGGCTTGCTTTCG 59.201 50.000 13.09 13.09 37.60 3.46
281 290 4.149922 GTCAACTCGATCGTCATTGACAAA 59.850 41.667 32.43 14.84 45.43 2.83
291 300 6.647212 TCGTCATTGACAAATCTGATACAC 57.353 37.500 16.61 0.00 32.09 2.90
299 308 6.700352 TGACAAATCTGATACACTCATGTGA 58.300 36.000 0.94 0.00 46.55 3.58
318 327 6.078456 TGTGATCCTTAATTCATGGGAACT 57.922 37.500 0.00 0.00 35.46 3.01
320 329 6.377996 TGTGATCCTTAATTCATGGGAACTTG 59.622 38.462 0.00 0.00 35.46 3.16
408 418 8.119845 GCCAGAAAACGTTCACAATTAAAATTT 58.880 29.630 0.00 0.00 36.09 1.82
417 427 7.305705 CGTTCACAATTAAAATTTCTGTTCGCA 60.306 33.333 0.00 0.00 0.00 5.10
443 453 3.678548 GGGTAAAGCGATCGATGGATAAC 59.321 47.826 21.57 9.80 31.51 1.89
444 454 4.557205 GGTAAAGCGATCGATGGATAACT 58.443 43.478 21.57 0.00 31.51 2.24
453 498 4.386867 TCGATGGATAACTCCTTCACAC 57.613 45.455 7.91 0.00 42.97 3.82
474 519 8.830580 TCACACGGTCTATATAAACACTAGTAC 58.169 37.037 0.00 0.00 0.00 2.73
475 520 7.795734 CACACGGTCTATATAAACACTAGTACG 59.204 40.741 0.00 0.00 0.00 3.67
478 523 6.310197 GGTCTATATAAACACTAGTACGCGG 58.690 44.000 12.47 0.00 0.00 6.46
550 611 1.412343 GAGTTGATCCTCCTCCTGCTC 59.588 57.143 0.00 0.00 0.00 4.26
560 621 3.746949 CTCCTGCTCCCCATGACGC 62.747 68.421 0.00 0.00 0.00 5.19
561 622 3.790437 CCTGCTCCCCATGACGCT 61.790 66.667 0.00 0.00 0.00 5.07
562 623 2.202987 CTGCTCCCCATGACGCTC 60.203 66.667 0.00 0.00 0.00 5.03
566 627 3.144120 CTCCCCATGACGCTCCTCG 62.144 68.421 0.00 0.00 45.38 4.63
641 702 4.179579 GCCTTGCCGCCGTCATTC 62.180 66.667 0.00 0.00 0.00 2.67
642 703 3.508840 CCTTGCCGCCGTCATTCC 61.509 66.667 0.00 0.00 0.00 3.01
643 704 3.864686 CTTGCCGCCGTCATTCCG 61.865 66.667 0.00 0.00 0.00 4.30
644 705 4.690719 TTGCCGCCGTCATTCCGT 62.691 61.111 0.00 0.00 0.00 4.69
1049 1116 2.023741 CATGTGCTTCGGCGATGC 59.976 61.111 32.84 32.84 45.37 3.91
1069 1136 2.037367 TGGACGCAGGCCTAGTCT 59.963 61.111 28.73 5.92 35.42 3.24
1183 1250 1.282875 GAACGGTGGAACAAGCTGC 59.717 57.895 0.00 0.00 44.16 5.25
1467 1534 2.346803 GCGAACTTGGTGAAGCATCTA 58.653 47.619 0.00 0.00 31.68 1.98
1468 1535 2.742053 GCGAACTTGGTGAAGCATCTAA 59.258 45.455 0.00 0.00 31.68 2.10
1480 1547 2.457598 AGCATCTAAACGTCCAGGAGA 58.542 47.619 0.00 0.00 0.00 3.71
1481 1548 2.832129 AGCATCTAAACGTCCAGGAGAA 59.168 45.455 0.00 0.00 0.00 2.87
1863 1949 9.888878 CTTATGATTTTGCATAACATACTCCTG 57.111 33.333 9.76 0.00 36.20 3.86
1871 1957 4.731773 GCATAACATACTCCTGTTGCAAGC 60.732 45.833 0.00 0.00 39.60 4.01
1926 2012 7.398618 TGGAATCCTCATATTTTAAGTTTGGCA 59.601 33.333 0.00 0.00 0.00 4.92
2015 2137 1.366366 CCTGAGGACCACGTCGTTT 59.634 57.895 0.00 0.00 32.65 3.60
2066 2188 1.230635 CGTGCAGTTCCAGTTGGAGG 61.231 60.000 0.51 0.00 46.36 4.30
2095 2217 2.338984 GACAAGACGTCGTGGGCT 59.661 61.111 30.30 13.68 34.19 5.19
2301 2423 0.680061 GAGTTTGAGTGGACGGAGGT 59.320 55.000 0.00 0.00 0.00 3.85
2389 2512 2.432628 GCTAAGCTCACGCCACGT 60.433 61.111 0.00 0.00 42.36 4.49
2409 2532 4.202599 ACGTAATAAGGGGGTTGGAACTTT 60.203 41.667 0.00 0.00 0.00 2.66
2427 2550 2.762535 TTAGGAGCCTTTTCAGACCG 57.237 50.000 0.00 0.00 0.00 4.79
2437 2560 3.561725 CCTTTTCAGACCGATGAATAGCC 59.438 47.826 8.72 0.00 38.90 3.93
2466 2589 7.148340 GGAGACAAGTCCTAAGAAACATCAATG 60.148 40.741 0.00 0.00 33.30 2.82
2472 2595 9.965902 AAGTCCTAAGAAACATCAATGATAAGT 57.034 29.630 0.00 0.00 0.00 2.24
2525 2651 1.186200 GGGGTTTTCTGCCTTCCATC 58.814 55.000 0.00 0.00 0.00 3.51
2537 2663 5.023533 TGCCTTCCATCATCTAAGTGTAC 57.976 43.478 0.00 0.00 0.00 2.90
2539 2665 5.897250 TGCCTTCCATCATCTAAGTGTACTA 59.103 40.000 0.00 0.00 0.00 1.82
2633 2759 5.361571 TCATATTAGTCTACCGCACAAAGGA 59.638 40.000 0.00 0.00 0.00 3.36
2638 2764 3.055094 AGTCTACCGCACAAAGGATCATT 60.055 43.478 0.00 0.00 0.00 2.57
2646 2772 4.339247 CGCACAAAGGATCATTTATTCCCT 59.661 41.667 4.82 0.00 32.05 4.20
2647 2773 5.594926 GCACAAAGGATCATTTATTCCCTG 58.405 41.667 4.82 0.00 32.05 4.45
2655 2781 8.050316 AGGATCATTTATTCCCTGACTGTATT 57.950 34.615 0.00 0.00 32.05 1.89
2656 2782 7.941238 AGGATCATTTATTCCCTGACTGTATTG 59.059 37.037 0.00 0.00 32.05 1.90
2657 2783 7.721399 GGATCATTTATTCCCTGACTGTATTGT 59.279 37.037 0.00 0.00 0.00 2.71
2658 2784 9.778741 GATCATTTATTCCCTGACTGTATTGTA 57.221 33.333 0.00 0.00 0.00 2.41
2659 2785 8.958119 TCATTTATTCCCTGACTGTATTGTAC 57.042 34.615 0.00 0.00 0.00 2.90
2660 2786 8.544622 TCATTTATTCCCTGACTGTATTGTACA 58.455 33.333 0.00 0.00 37.13 2.90
2697 2823 1.055849 ACATGTCTAGGTGGTGCACA 58.944 50.000 20.43 1.62 35.86 4.57
2720 2846 1.410882 CTCTGGCTAGAACTACAGGGC 59.589 57.143 0.00 0.00 31.21 5.19
2747 2873 1.626825 CTTCCCGACAACCCTCCTTTA 59.373 52.381 0.00 0.00 0.00 1.85
2766 2892 7.070629 TCCTTTACCTAAATTGAAAGGGTGTT 58.929 34.615 11.31 0.00 45.35 3.32
2781 2907 1.460689 TGTTGGTCCCCTCCTCGTT 60.461 57.895 0.00 0.00 0.00 3.85
2783 2909 2.221299 TTGGTCCCCTCCTCGTTGG 61.221 63.158 0.00 0.00 37.10 3.77
2804 2930 2.225293 GCCCCCTTTCCCTTCTTAGTTT 60.225 50.000 0.00 0.00 0.00 2.66
2828 2954 4.131376 CGAAGCATAGGCACCAGG 57.869 61.111 0.67 0.00 44.61 4.45
2829 2955 2.182842 CGAAGCATAGGCACCAGGC 61.183 63.158 0.67 0.00 44.61 4.85
2838 2964 4.648626 GCACCAGGCACCAGCAGA 62.649 66.667 0.00 0.00 44.61 4.26
2839 2965 2.359602 CACCAGGCACCAGCAGAG 60.360 66.667 0.00 0.00 44.61 3.35
2840 2966 2.851102 ACCAGGCACCAGCAGAGT 60.851 61.111 0.00 0.00 44.61 3.24
2841 2967 2.046507 CCAGGCACCAGCAGAGTC 60.047 66.667 0.00 0.00 44.61 3.36
2842 2968 2.591072 CCAGGCACCAGCAGAGTCT 61.591 63.158 0.00 0.00 44.61 3.24
2876 3002 3.643792 CCCAACACCAAAAATCCAACCTA 59.356 43.478 0.00 0.00 0.00 3.08
2910 3040 2.776963 CCCCATACACCCCCTCCC 60.777 72.222 0.00 0.00 0.00 4.30
2917 3047 0.865362 TACACCCCCTCCCTATCTCC 59.135 60.000 0.00 0.00 0.00 3.71
2925 3055 2.662633 CCCTCCCTATCTCCTCCCTAAT 59.337 54.545 0.00 0.00 0.00 1.73
2931 3061 6.110333 TCCCTATCTCCTCCCTAATACCTAA 58.890 44.000 0.00 0.00 0.00 2.69
2938 3068 5.845734 TCCTCCCTAATACCTAACAGTCAA 58.154 41.667 0.00 0.00 0.00 3.18
2946 3076 8.883731 CCTAATACCTAACAGTCAACATGAAAG 58.116 37.037 0.00 0.00 0.00 2.62
2980 3110 2.726832 ACGCACCTAGTTCTTGAGAC 57.273 50.000 0.00 0.00 0.00 3.36
2981 3111 1.272769 ACGCACCTAGTTCTTGAGACC 59.727 52.381 0.00 0.00 0.00 3.85
3010 3140 8.467402 AATAGATCCGACTTTGCTATTTATCG 57.533 34.615 0.00 0.00 30.00 2.92
3034 3164 9.157104 TCGTGTATCTTGAATTTTAGTGCATTA 57.843 29.630 0.00 0.00 0.00 1.90
3035 3165 9.935682 CGTGTATCTTGAATTTTAGTGCATTAT 57.064 29.630 0.00 0.00 0.00 1.28
3056 3186 0.984230 TTGAAGTCGAAGATGGGGCT 59.016 50.000 0.00 0.00 40.67 5.19
3057 3187 0.250234 TGAAGTCGAAGATGGGGCTG 59.750 55.000 0.00 0.00 40.67 4.85
3058 3188 1.078143 AAGTCGAAGATGGGGCTGC 60.078 57.895 0.00 0.00 40.67 5.25
3059 3189 1.841302 AAGTCGAAGATGGGGCTGCA 61.841 55.000 0.50 0.00 40.67 4.41
3073 3203 2.699073 CTGCATAATGAGCGGCAGT 58.301 52.632 1.45 0.00 46.47 4.40
3089 3219 1.910772 AGTGAGGAGCGCTGACCTT 60.911 57.895 18.48 0.00 36.57 3.50
3114 3244 3.435186 GCCGAGCCAAGACCTTGC 61.435 66.667 4.31 1.14 39.16 4.01
3119 3249 0.676151 GAGCCAAGACCTTGCTGGAG 60.676 60.000 4.31 0.00 39.16 3.86
3128 3258 1.254284 CCTTGCTGGAGACGAGGACT 61.254 60.000 0.00 0.00 38.35 3.85
3129 3259 1.464734 CTTGCTGGAGACGAGGACTA 58.535 55.000 0.00 0.00 0.00 2.59
3134 3264 0.538584 TGGAGACGAGGACTACGCTA 59.461 55.000 0.00 0.00 0.00 4.26
3139 3269 0.945813 ACGAGGACTACGCTATGAGC 59.054 55.000 0.00 0.00 38.02 4.26
3141 3271 2.224233 ACGAGGACTACGCTATGAGCTA 60.224 50.000 0.00 0.00 39.60 3.32
3145 3275 2.879646 GGACTACGCTATGAGCTACAGT 59.120 50.000 0.00 0.00 39.60 3.55
3154 3284 0.976641 TGAGCTACAGTGTCCCAAGG 59.023 55.000 0.00 0.00 0.00 3.61
3167 3297 3.017581 CAAGGTGGGAGGGGGAGG 61.018 72.222 0.00 0.00 0.00 4.30
3168 3298 4.371231 AAGGTGGGAGGGGGAGGG 62.371 72.222 0.00 0.00 0.00 4.30
3173 3303 4.825679 GGGAGGGGGAGGGGTCTG 62.826 77.778 0.00 0.00 0.00 3.51
3175 3305 2.125225 GAGGGGGAGGGGTCTGTT 59.875 66.667 0.00 0.00 0.00 3.16
3176 3306 1.996187 GAGGGGGAGGGGTCTGTTC 60.996 68.421 0.00 0.00 0.00 3.18
3177 3307 3.400054 GGGGGAGGGGTCTGTTCG 61.400 72.222 0.00 0.00 0.00 3.95
3178 3308 2.606826 GGGGAGGGGTCTGTTCGT 60.607 66.667 0.00 0.00 0.00 3.85
3179 3309 2.657066 GGGGAGGGGTCTGTTCGTC 61.657 68.421 0.00 0.00 0.00 4.20
3180 3310 1.911766 GGGAGGGGTCTGTTCGTCA 60.912 63.158 0.00 0.00 0.00 4.35
3196 3326 5.477291 TGTTCGTCAGAGAAGAAATAGAGGT 59.523 40.000 0.00 0.00 32.59 3.85
3198 3328 5.254115 TCGTCAGAGAAGAAATAGAGGTGA 58.746 41.667 0.00 0.00 0.00 4.02
3200 3330 5.124776 CGTCAGAGAAGAAATAGAGGTGAGT 59.875 44.000 0.00 0.00 0.00 3.41
3204 3334 7.670140 TCAGAGAAGAAATAGAGGTGAGTTACA 59.330 37.037 0.00 0.00 0.00 2.41
3211 3341 7.607991 AGAAATAGAGGTGAGTTACAATGGTTG 59.392 37.037 0.00 0.00 0.00 3.77
3232 3362 1.898574 GGCTTGGGCATATCGTGGG 60.899 63.158 0.00 0.00 40.87 4.61
3236 3366 1.618876 TTGGGCATATCGTGGGTCGT 61.619 55.000 0.00 0.00 40.80 4.34
3261 3391 2.030579 GCCGAGCGGAAGAAGAATAAAC 59.969 50.000 13.94 0.00 37.50 2.01
3262 3392 3.259064 CCGAGCGGAAGAAGAATAAACA 58.741 45.455 2.00 0.00 37.50 2.83
3263 3393 3.062234 CCGAGCGGAAGAAGAATAAACAC 59.938 47.826 2.00 0.00 37.50 3.32
3264 3394 3.927142 CGAGCGGAAGAAGAATAAACACT 59.073 43.478 0.00 0.00 0.00 3.55
3265 3395 5.100259 CGAGCGGAAGAAGAATAAACACTA 58.900 41.667 0.00 0.00 0.00 2.74
3266 3396 5.004535 CGAGCGGAAGAAGAATAAACACTAC 59.995 44.000 0.00 0.00 0.00 2.73
3267 3397 6.038997 AGCGGAAGAAGAATAAACACTACT 57.961 37.500 0.00 0.00 0.00 2.57
3268 3398 5.869888 AGCGGAAGAAGAATAAACACTACTG 59.130 40.000 0.00 0.00 0.00 2.74
3269 3399 5.063564 GCGGAAGAAGAATAAACACTACTGG 59.936 44.000 0.00 0.00 0.00 4.00
3270 3400 6.395629 CGGAAGAAGAATAAACACTACTGGA 58.604 40.000 0.00 0.00 0.00 3.86
3271 3401 6.872020 CGGAAGAAGAATAAACACTACTGGAA 59.128 38.462 0.00 0.00 0.00 3.53
3272 3402 7.549488 CGGAAGAAGAATAAACACTACTGGAAT 59.451 37.037 0.00 0.00 0.00 3.01
3273 3403 8.884726 GGAAGAAGAATAAACACTACTGGAATC 58.115 37.037 0.00 0.00 0.00 2.52
3274 3404 9.436957 GAAGAAGAATAAACACTACTGGAATCA 57.563 33.333 0.00 0.00 0.00 2.57
3275 3405 9.442047 AAGAAGAATAAACACTACTGGAATCAG 57.558 33.333 0.00 0.00 46.10 2.90
3276 3406 8.043710 AGAAGAATAAACACTACTGGAATCAGG 58.956 37.037 0.00 0.00 44.99 3.86
3277 3407 7.496346 AGAATAAACACTACTGGAATCAGGA 57.504 36.000 0.00 0.00 44.99 3.86
3278 3408 8.095452 AGAATAAACACTACTGGAATCAGGAT 57.905 34.615 0.00 0.00 44.99 3.24
3279 3409 8.207545 AGAATAAACACTACTGGAATCAGGATC 58.792 37.037 0.00 0.00 44.99 3.36
3280 3410 7.682787 ATAAACACTACTGGAATCAGGATCT 57.317 36.000 0.00 0.00 44.99 2.75
3281 3411 6.380079 AAACACTACTGGAATCAGGATCTT 57.620 37.500 0.00 0.00 44.99 2.40
3282 3412 6.380079 AACACTACTGGAATCAGGATCTTT 57.620 37.500 0.00 0.00 44.99 2.52
3283 3413 5.738909 ACACTACTGGAATCAGGATCTTTG 58.261 41.667 0.00 0.00 44.99 2.77
3284 3414 4.574013 CACTACTGGAATCAGGATCTTTGC 59.426 45.833 0.00 0.00 44.99 3.68
3285 3415 3.010200 ACTGGAATCAGGATCTTTGCC 57.990 47.619 0.00 0.00 44.99 4.52
3286 3416 1.945394 CTGGAATCAGGATCTTTGCCG 59.055 52.381 0.00 0.00 37.36 5.69
3287 3417 1.281867 TGGAATCAGGATCTTTGCCGT 59.718 47.619 0.00 0.00 0.00 5.68
3288 3418 1.943340 GGAATCAGGATCTTTGCCGTC 59.057 52.381 0.00 0.00 0.00 4.79
3289 3419 2.632377 GAATCAGGATCTTTGCCGTCA 58.368 47.619 0.00 0.00 0.00 4.35
3290 3420 2.322355 ATCAGGATCTTTGCCGTCAG 57.678 50.000 0.00 0.00 0.00 3.51
3291 3421 0.391661 TCAGGATCTTTGCCGTCAGC 60.392 55.000 0.00 0.00 44.14 4.26
3292 3422 1.078143 AGGATCTTTGCCGTCAGCC 60.078 57.895 0.00 0.00 42.71 4.85
3293 3423 2.464459 GGATCTTTGCCGTCAGCCG 61.464 63.158 0.00 0.00 42.71 5.52
3294 3424 3.100862 GATCTTTGCCGTCAGCCGC 62.101 63.158 0.00 0.00 42.71 6.53
3301 3431 3.121030 CCGTCAGCCGCCTCTTTG 61.121 66.667 0.00 0.00 34.38 2.77
3302 3432 3.793144 CGTCAGCCGCCTCTTTGC 61.793 66.667 0.00 0.00 0.00 3.68
3303 3433 3.435186 GTCAGCCGCCTCTTTGCC 61.435 66.667 0.00 0.00 0.00 4.52
3308 3438 3.121030 CCGCCTCTTTGCCGTCTG 61.121 66.667 0.00 0.00 0.00 3.51
3309 3439 3.793144 CGCCTCTTTGCCGTCTGC 61.793 66.667 0.00 0.00 41.77 4.26
3310 3440 2.359230 GCCTCTTTGCCGTCTGCT 60.359 61.111 0.00 0.00 42.00 4.24
3311 3441 1.079127 GCCTCTTTGCCGTCTGCTA 60.079 57.895 0.00 0.00 42.00 3.49
3312 3442 1.086634 GCCTCTTTGCCGTCTGCTAG 61.087 60.000 0.00 0.00 42.00 3.42
3313 3443 1.086634 CCTCTTTGCCGTCTGCTAGC 61.087 60.000 8.10 8.10 42.00 3.42
3314 3444 0.108424 CTCTTTGCCGTCTGCTAGCT 60.108 55.000 17.23 0.00 42.00 3.32
3315 3445 0.390340 TCTTTGCCGTCTGCTAGCTG 60.390 55.000 17.23 16.05 42.00 4.24
3316 3446 0.390340 CTTTGCCGTCTGCTAGCTGA 60.390 55.000 19.26 19.26 42.00 4.26
3317 3447 0.250234 TTTGCCGTCTGCTAGCTGAT 59.750 50.000 24.77 0.00 42.00 2.90
3318 3448 0.460811 TTGCCGTCTGCTAGCTGATG 60.461 55.000 27.97 27.97 42.00 3.07
3319 3449 1.593750 GCCGTCTGCTAGCTGATGG 60.594 63.158 39.01 39.01 46.93 3.51
3320 3450 1.593750 CCGTCTGCTAGCTGATGGC 60.594 63.158 35.80 20.19 41.70 4.40
3321 3451 1.142531 CGTCTGCTAGCTGATGGCA 59.857 57.895 27.50 3.46 44.09 4.92
3322 3452 0.460811 CGTCTGCTAGCTGATGGCAA 60.461 55.000 27.50 5.34 45.75 4.52
3323 3453 1.742761 GTCTGCTAGCTGATGGCAAA 58.257 50.000 24.77 0.46 45.75 3.68
3324 3454 1.669779 GTCTGCTAGCTGATGGCAAAG 59.330 52.381 24.77 7.05 45.75 2.77
3325 3455 1.556451 TCTGCTAGCTGATGGCAAAGA 59.444 47.619 19.26 5.91 45.75 2.52
3326 3456 2.026915 TCTGCTAGCTGATGGCAAAGAA 60.027 45.455 19.26 0.00 45.75 2.52
3327 3457 2.355132 CTGCTAGCTGATGGCAAAGAAG 59.645 50.000 17.23 0.00 45.75 2.85
3328 3458 1.674962 GCTAGCTGATGGCAAAGAAGG 59.325 52.381 7.70 0.00 44.79 3.46
3329 3459 2.943199 GCTAGCTGATGGCAAAGAAGGT 60.943 50.000 7.70 2.58 44.79 3.50
3330 3460 3.682718 GCTAGCTGATGGCAAAGAAGGTA 60.683 47.826 7.70 3.52 44.79 3.08
3331 3461 3.659183 AGCTGATGGCAAAGAAGGTAT 57.341 42.857 4.85 0.00 44.79 2.73
3332 3462 3.973425 AGCTGATGGCAAAGAAGGTATT 58.027 40.909 4.85 0.00 44.79 1.89
3333 3463 4.347607 AGCTGATGGCAAAGAAGGTATTT 58.652 39.130 4.85 0.00 44.79 1.40
3334 3464 4.159135 AGCTGATGGCAAAGAAGGTATTTG 59.841 41.667 4.85 0.00 44.79 2.32
3342 3472 4.427312 CAAAGAAGGTATTTGCCATCAGC 58.573 43.478 0.00 0.00 44.14 4.26
3343 3473 3.659183 AGAAGGTATTTGCCATCAGCT 57.341 42.857 0.00 0.00 44.23 4.24
3344 3474 3.973425 AGAAGGTATTTGCCATCAGCTT 58.027 40.909 0.00 0.00 44.23 3.74
3345 3475 5.116084 AGAAGGTATTTGCCATCAGCTTA 57.884 39.130 0.00 0.00 44.23 3.09
3346 3476 5.128919 AGAAGGTATTTGCCATCAGCTTAG 58.871 41.667 0.00 0.00 44.23 2.18
3347 3477 3.825328 AGGTATTTGCCATCAGCTTAGG 58.175 45.455 0.00 0.00 44.23 2.69
3348 3478 2.887152 GGTATTTGCCATCAGCTTAGGG 59.113 50.000 0.00 0.00 44.23 3.53
3349 3479 2.834638 ATTTGCCATCAGCTTAGGGT 57.165 45.000 0.00 0.00 44.23 4.34
3350 3480 1.838112 TTTGCCATCAGCTTAGGGTG 58.162 50.000 0.00 0.00 44.23 4.61
3351 3481 0.698238 TTGCCATCAGCTTAGGGTGT 59.302 50.000 3.81 0.00 44.23 4.16
3352 3482 0.035152 TGCCATCAGCTTAGGGTGTG 60.035 55.000 3.81 2.45 44.23 3.82
3353 3483 0.035056 GCCATCAGCTTAGGGTGTGT 60.035 55.000 3.81 0.00 41.24 3.72
3354 3484 1.614317 GCCATCAGCTTAGGGTGTGTT 60.614 52.381 3.81 0.00 41.24 3.32
3355 3485 2.795329 CCATCAGCTTAGGGTGTGTTT 58.205 47.619 3.81 0.00 41.24 2.83
3356 3486 2.489329 CCATCAGCTTAGGGTGTGTTTG 59.511 50.000 3.81 0.00 41.24 2.93
3357 3487 2.270352 TCAGCTTAGGGTGTGTTTGG 57.730 50.000 3.81 0.00 41.24 3.28
3358 3488 1.493022 TCAGCTTAGGGTGTGTTTGGT 59.507 47.619 3.81 0.00 41.24 3.67
3359 3489 2.706723 TCAGCTTAGGGTGTGTTTGGTA 59.293 45.455 3.81 0.00 41.24 3.25
3360 3490 3.074412 CAGCTTAGGGTGTGTTTGGTAG 58.926 50.000 0.00 0.00 36.34 3.18
3361 3491 2.039879 AGCTTAGGGTGTGTTTGGTAGG 59.960 50.000 0.00 0.00 0.00 3.18
3362 3492 2.878526 GCTTAGGGTGTGTTTGGTAGGG 60.879 54.545 0.00 0.00 0.00 3.53
3363 3493 2.121478 TAGGGTGTGTTTGGTAGGGT 57.879 50.000 0.00 0.00 0.00 4.34
3364 3494 0.476771 AGGGTGTGTTTGGTAGGGTG 59.523 55.000 0.00 0.00 0.00 4.61
3365 3495 1.176619 GGGTGTGTTTGGTAGGGTGC 61.177 60.000 0.00 0.00 0.00 5.01
3366 3496 0.466555 GGTGTGTTTGGTAGGGTGCA 60.467 55.000 0.00 0.00 0.00 4.57
3367 3497 1.616159 GTGTGTTTGGTAGGGTGCAT 58.384 50.000 0.00 0.00 0.00 3.96
3368 3498 1.269448 GTGTGTTTGGTAGGGTGCATG 59.731 52.381 0.00 0.00 0.00 4.06
3369 3499 1.143889 TGTGTTTGGTAGGGTGCATGA 59.856 47.619 0.00 0.00 0.00 3.07
3370 3500 2.235016 GTGTTTGGTAGGGTGCATGAA 58.765 47.619 0.00 0.00 0.00 2.57
3371 3501 2.228822 GTGTTTGGTAGGGTGCATGAAG 59.771 50.000 0.00 0.00 0.00 3.02
3372 3502 1.818674 GTTTGGTAGGGTGCATGAAGG 59.181 52.381 0.00 0.00 0.00 3.46
3373 3503 0.331278 TTGGTAGGGTGCATGAAGGG 59.669 55.000 0.00 0.00 0.00 3.95
3374 3504 0.844661 TGGTAGGGTGCATGAAGGGT 60.845 55.000 0.00 0.00 0.00 4.34
3375 3505 0.394352 GGTAGGGTGCATGAAGGGTG 60.394 60.000 0.00 0.00 0.00 4.61
3376 3506 1.032114 GTAGGGTGCATGAAGGGTGC 61.032 60.000 0.00 0.00 42.81 5.01
3381 3511 2.876581 TGCATGAAGGGTGCATGAG 58.123 52.632 7.68 0.00 46.76 2.90
3382 3512 0.328926 TGCATGAAGGGTGCATGAGA 59.671 50.000 7.68 0.00 46.76 3.27
3383 3513 1.022735 GCATGAAGGGTGCATGAGAG 58.977 55.000 7.68 0.00 44.49 3.20
3384 3514 1.681166 GCATGAAGGGTGCATGAGAGT 60.681 52.381 7.68 0.00 44.49 3.24
3385 3515 2.420547 GCATGAAGGGTGCATGAGAGTA 60.421 50.000 7.68 0.00 44.49 2.59
3386 3516 3.877559 CATGAAGGGTGCATGAGAGTAA 58.122 45.455 0.00 0.00 44.49 2.24
3387 3517 4.264253 CATGAAGGGTGCATGAGAGTAAA 58.736 43.478 0.00 0.00 44.49 2.01
3388 3518 4.365514 TGAAGGGTGCATGAGAGTAAAA 57.634 40.909 0.00 0.00 0.00 1.52
3389 3519 4.326826 TGAAGGGTGCATGAGAGTAAAAG 58.673 43.478 0.00 0.00 0.00 2.27
3390 3520 4.202461 TGAAGGGTGCATGAGAGTAAAAGT 60.202 41.667 0.00 0.00 0.00 2.66
3391 3521 4.373156 AGGGTGCATGAGAGTAAAAGTT 57.627 40.909 0.00 0.00 0.00 2.66
3392 3522 4.327680 AGGGTGCATGAGAGTAAAAGTTC 58.672 43.478 0.00 0.00 0.00 3.01
3393 3523 3.440522 GGGTGCATGAGAGTAAAAGTTCC 59.559 47.826 0.00 0.00 0.00 3.62
3394 3524 3.440522 GGTGCATGAGAGTAAAAGTTCCC 59.559 47.826 0.00 0.00 0.00 3.97
3395 3525 4.327680 GTGCATGAGAGTAAAAGTTCCCT 58.672 43.478 0.00 0.00 0.00 4.20
3396 3526 4.762251 GTGCATGAGAGTAAAAGTTCCCTT 59.238 41.667 0.00 0.00 0.00 3.95
3397 3527 5.003804 TGCATGAGAGTAAAAGTTCCCTTC 58.996 41.667 0.00 0.00 0.00 3.46
3398 3528 5.221925 TGCATGAGAGTAAAAGTTCCCTTCT 60.222 40.000 0.00 0.00 0.00 2.85
3399 3529 5.707764 GCATGAGAGTAAAAGTTCCCTTCTT 59.292 40.000 0.00 0.00 0.00 2.52
3400 3530 6.348868 GCATGAGAGTAAAAGTTCCCTTCTTG 60.349 42.308 0.00 0.00 0.00 3.02
3401 3531 6.494666 TGAGAGTAAAAGTTCCCTTCTTGA 57.505 37.500 0.00 0.00 0.00 3.02
3402 3532 6.289064 TGAGAGTAAAAGTTCCCTTCTTGAC 58.711 40.000 0.00 0.00 0.00 3.18
3403 3533 5.622180 AGAGTAAAAGTTCCCTTCTTGACC 58.378 41.667 0.00 0.00 0.00 4.02
3404 3534 4.726583 AGTAAAAGTTCCCTTCTTGACCC 58.273 43.478 0.00 0.00 0.00 4.46
3405 3535 3.680777 AAAAGTTCCCTTCTTGACCCA 57.319 42.857 0.00 0.00 0.00 4.51
3406 3536 2.658807 AAGTTCCCTTCTTGACCCAC 57.341 50.000 0.00 0.00 0.00 4.61
3407 3537 1.821088 AGTTCCCTTCTTGACCCACT 58.179 50.000 0.00 0.00 0.00 4.00
3408 3538 2.136026 AGTTCCCTTCTTGACCCACTT 58.864 47.619 0.00 0.00 0.00 3.16
3409 3539 2.514160 AGTTCCCTTCTTGACCCACTTT 59.486 45.455 0.00 0.00 0.00 2.66
3410 3540 3.052869 AGTTCCCTTCTTGACCCACTTTT 60.053 43.478 0.00 0.00 0.00 2.27
3411 3541 2.944129 TCCCTTCTTGACCCACTTTTG 58.056 47.619 0.00 0.00 0.00 2.44
3412 3542 2.243736 TCCCTTCTTGACCCACTTTTGT 59.756 45.455 0.00 0.00 0.00 2.83
3426 3556 5.560966 CACTTTTGTGTGTTTGGTAGAGT 57.439 39.130 0.00 0.00 44.94 3.24
3427 3557 5.331902 CACTTTTGTGTGTTTGGTAGAGTG 58.668 41.667 0.00 0.00 44.94 3.51
3428 3558 5.007682 ACTTTTGTGTGTTTGGTAGAGTGT 58.992 37.500 0.00 0.00 0.00 3.55
3429 3559 6.092944 CACTTTTGTGTGTTTGGTAGAGTGTA 59.907 38.462 0.00 0.00 44.94 2.90
3430 3560 6.826741 ACTTTTGTGTGTTTGGTAGAGTGTAT 59.173 34.615 0.00 0.00 0.00 2.29
3431 3561 6.612247 TTTGTGTGTTTGGTAGAGTGTATG 57.388 37.500 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.367444 TGCTTAAAATCGGTTAAAAACAAGAAA 57.633 25.926 0.00 0.00 0.00 2.52
10 11 8.928270 TGCTTAAAATCGGTTAAAAACAAGAA 57.072 26.923 0.00 0.00 0.00 2.52
11 12 8.928270 TTGCTTAAAATCGGTTAAAAACAAGA 57.072 26.923 0.00 0.00 0.00 3.02
12 13 9.416058 GTTTGCTTAAAATCGGTTAAAAACAAG 57.584 29.630 0.00 0.00 30.75 3.16
13 14 8.108782 CGTTTGCTTAAAATCGGTTAAAAACAA 58.891 29.630 0.00 0.00 30.25 2.83
14 15 7.275123 ACGTTTGCTTAAAATCGGTTAAAAACA 59.725 29.630 0.00 0.00 30.25 2.83
15 16 7.576248 CACGTTTGCTTAAAATCGGTTAAAAAC 59.424 33.333 0.00 0.00 31.09 2.43
16 17 7.275123 ACACGTTTGCTTAAAATCGGTTAAAAA 59.725 29.630 0.00 0.00 31.09 1.94
40 41 5.908916 TCGTGTTCGAAAATTATGTCACA 57.091 34.783 0.00 0.00 43.34 3.58
95 96 6.674694 AGAGCAAGCTATGATTTAGTGTTG 57.325 37.500 0.00 0.00 0.00 3.33
96 97 6.881065 TGAAGAGCAAGCTATGATTTAGTGTT 59.119 34.615 0.00 0.00 0.00 3.32
97 98 6.409704 TGAAGAGCAAGCTATGATTTAGTGT 58.590 36.000 0.00 0.00 0.00 3.55
98 99 6.915544 TGAAGAGCAAGCTATGATTTAGTG 57.084 37.500 0.00 0.00 0.00 2.74
100 101 8.380743 AGAATGAAGAGCAAGCTATGATTTAG 57.619 34.615 0.00 0.00 0.00 1.85
104 111 6.423302 CGTTAGAATGAAGAGCAAGCTATGAT 59.577 38.462 0.00 0.00 0.00 2.45
115 122 6.978659 TGCTATGGTAACGTTAGAATGAAGAG 59.021 38.462 8.60 1.60 42.51 2.85
163 170 1.609061 CCACCTCGACTTGCTTCACAT 60.609 52.381 0.00 0.00 0.00 3.21
167 174 0.674895 ATGCCACCTCGACTTGCTTC 60.675 55.000 0.00 0.00 0.00 3.86
253 262 2.929960 TGACGATCGAGTTGACAAGTC 58.070 47.619 24.34 12.29 0.00 3.01
281 290 6.744175 AAGGATCACATGAGTGTATCAGAT 57.256 37.500 0.00 0.00 46.01 2.90
291 300 6.301486 TCCCATGAATTAAGGATCACATGAG 58.699 40.000 0.00 0.00 35.94 2.90
299 308 6.953520 TGTTCAAGTTCCCATGAATTAAGGAT 59.046 34.615 0.00 0.00 37.82 3.24
389 399 8.528295 CGAACAGAAATTTTAATTGTGAACGTT 58.472 29.630 0.00 0.00 0.00 3.99
408 418 2.935238 GCTTTACCCAGATGCGAACAGA 60.935 50.000 0.00 0.00 0.00 3.41
417 427 2.289072 CCATCGATCGCTTTACCCAGAT 60.289 50.000 11.09 0.00 0.00 2.90
443 453 6.696148 GTGTTTATATAGACCGTGTGAAGGAG 59.304 42.308 1.24 0.00 0.00 3.69
444 454 6.379133 AGTGTTTATATAGACCGTGTGAAGGA 59.621 38.462 1.24 0.00 0.00 3.36
453 498 6.011879 CGCGTACTAGTGTTTATATAGACCG 58.988 44.000 5.39 0.00 0.00 4.79
474 519 2.587322 TACTTCCCCTTCATGCCGCG 62.587 60.000 0.00 0.00 0.00 6.46
475 520 0.815615 CTACTTCCCCTTCATGCCGC 60.816 60.000 0.00 0.00 0.00 6.53
478 523 1.673168 CTGCTACTTCCCCTTCATGC 58.327 55.000 0.00 0.00 0.00 4.06
511 564 4.758251 TGCATGGCGTGACCGGAG 62.758 66.667 9.46 0.00 43.94 4.63
560 621 1.012124 CGATGACGACGACGAGGAG 60.012 63.158 15.32 0.00 42.66 3.69
561 622 2.458610 CCGATGACGACGACGAGGA 61.459 63.158 15.32 0.00 42.66 3.71
562 623 2.022902 CCGATGACGACGACGAGG 59.977 66.667 15.32 5.35 42.66 4.63
566 627 3.248171 GCTGCCGATGACGACGAC 61.248 66.667 0.00 0.00 42.66 4.34
639 700 1.812686 CGAGACCCCACTTGACGGAA 61.813 60.000 0.00 0.00 0.00 4.30
640 701 2.273179 CGAGACCCCACTTGACGGA 61.273 63.158 0.00 0.00 0.00 4.69
641 702 1.246056 TACGAGACCCCACTTGACGG 61.246 60.000 0.00 0.00 0.00 4.79
642 703 0.109412 GTACGAGACCCCACTTGACG 60.109 60.000 0.00 0.00 0.00 4.35
643 704 0.109412 CGTACGAGACCCCACTTGAC 60.109 60.000 10.44 0.00 0.00 3.18
644 705 0.538057 ACGTACGAGACCCCACTTGA 60.538 55.000 24.41 0.00 0.00 3.02
645 706 0.388134 CACGTACGAGACCCCACTTG 60.388 60.000 24.41 1.10 0.00 3.16
646 707 0.538057 TCACGTACGAGACCCCACTT 60.538 55.000 24.41 0.00 0.00 3.16
956 1017 0.776451 GTCGTTAGACGTGCACTGTG 59.224 55.000 16.19 2.76 43.14 3.66
1049 1116 4.514577 CTAGGCCTGCGTCCACGG 62.515 72.222 17.99 0.00 40.23 4.94
1053 1120 2.496817 CAGACTAGGCCTGCGTCC 59.503 66.667 24.99 12.87 0.00 4.79
1131 1198 4.681978 GTCAACGCCGGGAGTGCT 62.682 66.667 3.56 0.00 0.00 4.40
1467 1534 0.033090 GGACGTTCTCCTGGACGTTT 59.967 55.000 12.50 0.00 39.02 3.60
1468 1535 1.664306 GGACGTTCTCCTGGACGTT 59.336 57.895 12.50 0.00 39.02 3.99
1480 1547 0.107800 TCGATCTCTCTCCGGACGTT 60.108 55.000 0.00 0.00 0.00 3.99
1481 1548 0.531090 CTCGATCTCTCTCCGGACGT 60.531 60.000 0.00 0.00 0.00 4.34
1522 1589 2.283676 TTCCTCGCCGACCTCCTT 60.284 61.111 0.00 0.00 0.00 3.36
1854 1926 4.194640 AGTATGCTTGCAACAGGAGTATG 58.805 43.478 0.00 0.00 0.00 2.39
1858 1930 2.012673 GGAGTATGCTTGCAACAGGAG 58.987 52.381 0.00 0.00 0.00 3.69
1863 1949 3.923017 AAAGTGGAGTATGCTTGCAAC 57.077 42.857 0.00 0.13 0.00 4.17
1899 1985 8.424133 GCCAAACTTAAAATATGAGGATTCCAT 58.576 33.333 5.29 0.00 0.00 3.41
1900 1986 7.398618 TGCCAAACTTAAAATATGAGGATTCCA 59.601 33.333 5.29 0.00 0.00 3.53
1901 1987 7.781056 TGCCAAACTTAAAATATGAGGATTCC 58.219 34.615 0.00 0.00 0.00 3.01
1943 2029 3.704566 TGTGTGACCTTGACTGACTAACT 59.295 43.478 0.00 0.00 0.00 2.24
1999 2121 0.531090 CCAAAACGACGTGGTCCTCA 60.531 55.000 2.90 0.00 0.00 3.86
2066 2188 4.410400 CTTGTCCCGCCCCAGACC 62.410 72.222 0.00 0.00 31.76 3.85
2095 2217 1.003580 GGCTGAAACTCATCTGGGTCA 59.996 52.381 0.00 0.00 0.00 4.02
2301 2423 2.046023 CAGCCATGTCGCCTTCCA 60.046 61.111 0.00 0.00 0.00 3.53
2389 2512 5.796928 TCCTAAAGTTCCAACCCCCTTATTA 59.203 40.000 0.00 0.00 0.00 0.98
2409 2532 1.933021 TCGGTCTGAAAAGGCTCCTA 58.067 50.000 0.00 0.00 0.00 2.94
2427 2550 4.712476 ACTTGTCTCCATGGCTATTCATC 58.288 43.478 6.96 0.00 0.00 2.92
2437 2560 5.551233 TGTTTCTTAGGACTTGTCTCCATG 58.449 41.667 0.61 0.00 31.94 3.66
2550 2676 9.726438 ACAAGTCAAGCAATAAACTTAGATAGT 57.274 29.630 0.00 0.00 39.32 2.12
2623 2749 4.339247 AGGGAATAAATGATCCTTTGTGCG 59.661 41.667 6.26 0.00 35.95 5.34
2633 2759 9.561069 GTACAATACAGTCAGGGAATAAATGAT 57.439 33.333 0.00 0.00 0.00 2.45
2638 2764 7.857456 ACATGTACAATACAGTCAGGGAATAA 58.143 34.615 0.00 0.00 42.77 1.40
2646 2772 4.407621 CCCCCTACATGTACAATACAGTCA 59.592 45.833 0.08 0.00 42.77 3.41
2647 2773 4.957296 CCCCCTACATGTACAATACAGTC 58.043 47.826 0.08 0.00 42.77 3.51
2677 2803 1.419762 TGTGCACCACCTAGACATGTT 59.580 47.619 15.69 0.00 32.73 2.71
2697 2823 3.093057 CCTGTAGTTCTAGCCAGAGTGT 58.907 50.000 0.00 0.00 30.73 3.55
2699 2825 2.741145 CCCTGTAGTTCTAGCCAGAGT 58.259 52.381 0.00 0.00 30.73 3.24
2704 2830 1.227292 GCGCCCTGTAGTTCTAGCC 60.227 63.158 0.00 0.00 0.00 3.93
2727 2853 0.400594 AAAGGAGGGTTGTCGGGAAG 59.599 55.000 0.00 0.00 0.00 3.46
2730 2856 0.035725 GGTAAAGGAGGGTTGTCGGG 60.036 60.000 0.00 0.00 0.00 5.14
2747 2873 4.552674 ACCAACACCCTTTCAATTTAGGT 58.447 39.130 0.00 0.00 0.00 3.08
2781 2907 0.478789 TAAGAAGGGAAAGGGGGCCA 60.479 55.000 4.39 0.00 0.00 5.36
2783 2909 1.000496 ACTAAGAAGGGAAAGGGGGC 59.000 55.000 0.00 0.00 0.00 5.80
2787 2913 4.558697 CGCCAAAAACTAAGAAGGGAAAGG 60.559 45.833 0.00 0.00 0.00 3.11
2804 2930 2.760159 GCCTATGCTTCGCGCCAAA 61.760 57.895 0.00 0.00 38.05 3.28
2828 2954 1.072159 ACCAAGACTCTGCTGGTGC 59.928 57.895 2.08 0.00 40.20 5.01
2829 2955 2.924185 CACCAAGACTCTGCTGGTG 58.076 57.895 13.31 13.31 43.06 4.17
2830 2956 1.717032 TACACCAAGACTCTGCTGGT 58.283 50.000 0.00 0.00 0.00 4.00
2831 2957 2.839486 TTACACCAAGACTCTGCTGG 57.161 50.000 0.00 0.00 0.00 4.85
2832 2958 4.154918 GGAATTTACACCAAGACTCTGCTG 59.845 45.833 0.00 0.00 0.00 4.41
2833 2959 4.327680 GGAATTTACACCAAGACTCTGCT 58.672 43.478 0.00 0.00 0.00 4.24
2834 2960 3.440522 GGGAATTTACACCAAGACTCTGC 59.559 47.826 0.00 0.00 0.00 4.26
2835 2961 4.651778 TGGGAATTTACACCAAGACTCTG 58.348 43.478 0.00 0.00 0.00 3.35
2836 2962 4.993705 TGGGAATTTACACCAAGACTCT 57.006 40.909 0.00 0.00 0.00 3.24
2837 2963 4.825085 TGTTGGGAATTTACACCAAGACTC 59.175 41.667 0.00 0.00 44.27 3.36
2838 2964 4.798882 TGTTGGGAATTTACACCAAGACT 58.201 39.130 0.00 0.00 44.27 3.24
2839 2965 4.866921 GTGTTGGGAATTTACACCAAGAC 58.133 43.478 12.92 12.92 46.59 3.01
2866 2992 1.607225 TCCCATGCCTAGGTTGGATT 58.393 50.000 26.05 0.00 31.94 3.01
2868 2994 1.140312 GATCCCATGCCTAGGTTGGA 58.860 55.000 26.05 18.98 31.94 3.53
2876 3002 0.325577 GGGTTTTGGATCCCATGCCT 60.326 55.000 9.90 0.00 42.95 4.75
2899 3025 0.936863 AGGAGATAGGGAGGGGGTGT 60.937 60.000 0.00 0.00 0.00 4.16
2910 3040 7.471890 ACTGTTAGGTATTAGGGAGGAGATAG 58.528 42.308 0.00 0.00 0.00 2.08
2917 3047 6.540438 TGTTGACTGTTAGGTATTAGGGAG 57.460 41.667 0.00 0.00 0.00 4.30
2925 3055 5.001232 GCCTTTCATGTTGACTGTTAGGTA 58.999 41.667 0.00 0.00 0.00 3.08
2931 3061 2.508526 GGAGCCTTTCATGTTGACTGT 58.491 47.619 0.00 0.00 0.00 3.55
2938 3068 0.706433 ACCATGGGAGCCTTTCATGT 59.294 50.000 18.09 0.00 37.24 3.21
2946 3076 2.189521 CGTACCACCATGGGAGCC 59.810 66.667 18.09 0.00 43.37 4.70
2980 3110 3.871594 AGCAAAGTCGGATCTATTTTCGG 59.128 43.478 0.00 0.00 0.00 4.30
2981 3111 6.771188 ATAGCAAAGTCGGATCTATTTTCG 57.229 37.500 0.00 0.00 0.00 3.46
3029 3159 5.504665 CCCATCTTCGACTTCAACATAATGC 60.505 44.000 0.00 0.00 0.00 3.56
3034 3164 2.941415 GCCCCATCTTCGACTTCAACAT 60.941 50.000 0.00 0.00 0.00 2.71
3035 3165 1.610624 GCCCCATCTTCGACTTCAACA 60.611 52.381 0.00 0.00 0.00 3.33
3056 3186 0.107752 TCACTGCCGCTCATTATGCA 60.108 50.000 0.00 0.00 0.00 3.96
3057 3187 0.585357 CTCACTGCCGCTCATTATGC 59.415 55.000 0.00 0.00 0.00 3.14
3058 3188 1.202568 TCCTCACTGCCGCTCATTATG 60.203 52.381 0.00 0.00 0.00 1.90
3059 3189 1.069823 CTCCTCACTGCCGCTCATTAT 59.930 52.381 0.00 0.00 0.00 1.28
3073 3203 1.004560 CAAAGGTCAGCGCTCCTCA 60.005 57.895 17.30 0.00 33.09 3.86
3083 3213 4.697756 CGGCCTCGGCAAAGGTCA 62.698 66.667 10.51 0.00 41.36 4.02
3085 3215 4.394712 CTCGGCCTCGGCAAAGGT 62.395 66.667 10.51 0.00 44.11 3.50
3104 3234 0.318441 TCGTCTCCAGCAAGGTCTTG 59.682 55.000 6.36 6.36 43.14 3.02
3106 3236 1.254284 CCTCGTCTCCAGCAAGGTCT 61.254 60.000 0.00 0.00 39.02 3.85
3114 3244 0.745128 AGCGTAGTCCTCGTCTCCAG 60.745 60.000 0.00 0.00 0.00 3.86
3119 3249 1.069771 GCTCATAGCGTAGTCCTCGTC 60.070 57.143 0.00 0.00 0.00 4.20
3134 3264 1.556911 CCTTGGGACACTGTAGCTCAT 59.443 52.381 0.00 0.00 39.29 2.90
3139 3269 3.935993 CCACCTTGGGACACTGTAG 57.064 57.895 0.00 0.00 39.29 2.74
3159 3289 2.125225 GAACAGACCCCTCCCCCT 59.875 66.667 0.00 0.00 0.00 4.79
3162 3292 1.911766 TGACGAACAGACCCCTCCC 60.912 63.158 0.00 0.00 0.00 4.30
3172 3302 5.477291 ACCTCTATTTCTTCTCTGACGAACA 59.523 40.000 0.00 0.00 0.00 3.18
3173 3303 5.802956 CACCTCTATTTCTTCTCTGACGAAC 59.197 44.000 0.00 0.00 0.00 3.95
3175 3305 5.254115 TCACCTCTATTTCTTCTCTGACGA 58.746 41.667 0.00 0.00 0.00 4.20
3176 3306 5.124776 ACTCACCTCTATTTCTTCTCTGACG 59.875 44.000 0.00 0.00 0.00 4.35
3177 3307 6.524101 ACTCACCTCTATTTCTTCTCTGAC 57.476 41.667 0.00 0.00 0.00 3.51
3178 3308 7.670140 TGTAACTCACCTCTATTTCTTCTCTGA 59.330 37.037 0.00 0.00 0.00 3.27
3179 3309 7.831753 TGTAACTCACCTCTATTTCTTCTCTG 58.168 38.462 0.00 0.00 0.00 3.35
3180 3310 8.423906 TTGTAACTCACCTCTATTTCTTCTCT 57.576 34.615 0.00 0.00 0.00 3.10
3189 3319 5.250774 ACCAACCATTGTAACTCACCTCTAT 59.749 40.000 0.00 0.00 0.00 1.98
3196 3326 2.158534 AGCCACCAACCATTGTAACTCA 60.159 45.455 0.00 0.00 0.00 3.41
3198 3328 2.627699 CAAGCCACCAACCATTGTAACT 59.372 45.455 0.00 0.00 0.00 2.24
3200 3330 1.967066 CCAAGCCACCAACCATTGTAA 59.033 47.619 0.00 0.00 0.00 2.41
3204 3334 2.216331 GCCCAAGCCACCAACCATT 61.216 57.895 0.00 0.00 0.00 3.16
3211 3341 1.152963 ACGATATGCCCAAGCCACC 60.153 57.895 0.00 0.00 38.69 4.61
3261 3391 4.574013 GCAAAGATCCTGATTCCAGTAGTG 59.426 45.833 0.00 0.00 38.74 2.74
3262 3392 4.384647 GGCAAAGATCCTGATTCCAGTAGT 60.385 45.833 0.00 0.00 38.74 2.73
3263 3393 4.133078 GGCAAAGATCCTGATTCCAGTAG 58.867 47.826 0.00 0.00 38.74 2.57
3264 3394 3.432186 CGGCAAAGATCCTGATTCCAGTA 60.432 47.826 0.00 0.00 38.74 2.74
3265 3395 2.681976 CGGCAAAGATCCTGATTCCAGT 60.682 50.000 0.00 0.00 38.74 4.00
3266 3396 1.945394 CGGCAAAGATCCTGATTCCAG 59.055 52.381 0.00 0.00 40.09 3.86
3267 3397 1.281867 ACGGCAAAGATCCTGATTCCA 59.718 47.619 0.00 0.00 0.00 3.53
3268 3398 1.943340 GACGGCAAAGATCCTGATTCC 59.057 52.381 0.00 0.00 0.00 3.01
3269 3399 2.611292 CTGACGGCAAAGATCCTGATTC 59.389 50.000 0.00 0.00 0.00 2.52
3270 3400 2.636830 CTGACGGCAAAGATCCTGATT 58.363 47.619 0.00 0.00 0.00 2.57
3271 3401 1.745141 GCTGACGGCAAAGATCCTGAT 60.745 52.381 0.00 0.00 41.35 2.90
3272 3402 0.391661 GCTGACGGCAAAGATCCTGA 60.392 55.000 0.00 0.00 41.35 3.86
3273 3403 1.372087 GGCTGACGGCAAAGATCCTG 61.372 60.000 8.86 0.00 44.01 3.86
3274 3404 1.078143 GGCTGACGGCAAAGATCCT 60.078 57.895 8.86 0.00 44.01 3.24
3275 3405 2.464459 CGGCTGACGGCAAAGATCC 61.464 63.158 8.86 0.00 44.01 3.36
3276 3406 3.093278 CGGCTGACGGCAAAGATC 58.907 61.111 8.86 0.00 44.01 2.75
3277 3407 3.127533 GCGGCTGACGGCAAAGAT 61.128 61.111 4.52 0.00 44.51 2.40
3284 3414 3.121030 CAAAGAGGCGGCTGACGG 61.121 66.667 19.63 0.00 44.51 4.79
3286 3416 3.435186 GGCAAAGAGGCGGCTGAC 61.435 66.667 19.63 0.00 33.57 3.51
3301 3431 1.593750 CCATCAGCTAGCAGACGGC 60.594 63.158 18.83 0.00 45.30 5.68
3302 3432 1.593750 GCCATCAGCTAGCAGACGG 60.594 63.158 17.03 17.03 38.99 4.79
3303 3433 0.460811 TTGCCATCAGCTAGCAGACG 60.461 55.000 18.83 6.89 44.23 4.18
3304 3434 1.669779 CTTTGCCATCAGCTAGCAGAC 59.330 52.381 18.83 3.34 44.23 3.51
3305 3435 1.556451 TCTTTGCCATCAGCTAGCAGA 59.444 47.619 18.83 15.64 44.23 4.26
3306 3436 2.034104 TCTTTGCCATCAGCTAGCAG 57.966 50.000 18.83 9.54 44.23 4.24
3307 3437 2.362736 CTTCTTTGCCATCAGCTAGCA 58.637 47.619 18.83 0.00 44.23 3.49
3308 3438 1.674962 CCTTCTTTGCCATCAGCTAGC 59.325 52.381 6.62 6.62 44.23 3.42
3309 3439 2.996631 ACCTTCTTTGCCATCAGCTAG 58.003 47.619 0.00 0.00 44.23 3.42
3310 3440 4.778213 ATACCTTCTTTGCCATCAGCTA 57.222 40.909 0.00 0.00 44.23 3.32
3311 3441 3.659183 ATACCTTCTTTGCCATCAGCT 57.341 42.857 0.00 0.00 44.23 4.24
3312 3442 4.427312 CAAATACCTTCTTTGCCATCAGC 58.573 43.478 0.00 0.00 44.14 4.26
3320 3450 4.159135 AGCTGATGGCAAATACCTTCTTTG 59.841 41.667 0.00 0.00 44.79 2.77
3321 3451 4.347607 AGCTGATGGCAAATACCTTCTTT 58.652 39.130 0.00 0.00 44.79 2.52
3322 3452 3.973425 AGCTGATGGCAAATACCTTCTT 58.027 40.909 0.00 0.00 44.79 2.52
3323 3453 3.659183 AGCTGATGGCAAATACCTTCT 57.341 42.857 0.00 0.00 44.79 2.85
3324 3454 4.276926 CCTAAGCTGATGGCAAATACCTTC 59.723 45.833 0.00 0.00 44.79 3.46
3325 3455 4.210331 CCTAAGCTGATGGCAAATACCTT 58.790 43.478 0.00 0.00 44.79 3.50
3326 3456 3.435601 CCCTAAGCTGATGGCAAATACCT 60.436 47.826 0.00 0.00 44.79 3.08
3327 3457 2.887152 CCCTAAGCTGATGGCAAATACC 59.113 50.000 0.00 0.00 44.79 2.73
3328 3458 3.316308 CACCCTAAGCTGATGGCAAATAC 59.684 47.826 0.00 0.00 44.79 1.89
3329 3459 3.053693 ACACCCTAAGCTGATGGCAAATA 60.054 43.478 0.00 0.00 44.79 1.40
3330 3460 2.291800 ACACCCTAAGCTGATGGCAAAT 60.292 45.455 0.00 0.00 44.79 2.32
3331 3461 1.075374 ACACCCTAAGCTGATGGCAAA 59.925 47.619 0.00 0.00 44.79 3.68
3332 3462 0.698238 ACACCCTAAGCTGATGGCAA 59.302 50.000 0.00 0.00 44.79 4.52
3333 3463 0.035152 CACACCCTAAGCTGATGGCA 60.035 55.000 0.00 0.00 44.79 4.92
3334 3464 0.035056 ACACACCCTAAGCTGATGGC 60.035 55.000 0.00 0.00 42.19 4.40
3335 3465 2.489329 CAAACACACCCTAAGCTGATGG 59.511 50.000 0.00 0.00 0.00 3.51
3336 3466 2.489329 CCAAACACACCCTAAGCTGATG 59.511 50.000 0.00 0.00 0.00 3.07
3337 3467 2.108250 ACCAAACACACCCTAAGCTGAT 59.892 45.455 0.00 0.00 0.00 2.90
3338 3468 1.493022 ACCAAACACACCCTAAGCTGA 59.507 47.619 0.00 0.00 0.00 4.26
3339 3469 1.981256 ACCAAACACACCCTAAGCTG 58.019 50.000 0.00 0.00 0.00 4.24
3340 3470 2.039879 CCTACCAAACACACCCTAAGCT 59.960 50.000 0.00 0.00 0.00 3.74
3341 3471 2.433436 CCTACCAAACACACCCTAAGC 58.567 52.381 0.00 0.00 0.00 3.09
3342 3472 2.374170 ACCCTACCAAACACACCCTAAG 59.626 50.000 0.00 0.00 0.00 2.18
3343 3473 2.106857 CACCCTACCAAACACACCCTAA 59.893 50.000 0.00 0.00 0.00 2.69
3344 3474 1.700739 CACCCTACCAAACACACCCTA 59.299 52.381 0.00 0.00 0.00 3.53
3345 3475 0.476771 CACCCTACCAAACACACCCT 59.523 55.000 0.00 0.00 0.00 4.34
3346 3476 1.176619 GCACCCTACCAAACACACCC 61.177 60.000 0.00 0.00 0.00 4.61
3347 3477 0.466555 TGCACCCTACCAAACACACC 60.467 55.000 0.00 0.00 0.00 4.16
3348 3478 1.269448 CATGCACCCTACCAAACACAC 59.731 52.381 0.00 0.00 0.00 3.82
3349 3479 1.143889 TCATGCACCCTACCAAACACA 59.856 47.619 0.00 0.00 0.00 3.72
3350 3480 1.904287 TCATGCACCCTACCAAACAC 58.096 50.000 0.00 0.00 0.00 3.32
3351 3481 2.513753 CTTCATGCACCCTACCAAACA 58.486 47.619 0.00 0.00 0.00 2.83
3352 3482 1.818674 CCTTCATGCACCCTACCAAAC 59.181 52.381 0.00 0.00 0.00 2.93
3353 3483 1.272425 CCCTTCATGCACCCTACCAAA 60.272 52.381 0.00 0.00 0.00 3.28
3354 3484 0.331278 CCCTTCATGCACCCTACCAA 59.669 55.000 0.00 0.00 0.00 3.67
3355 3485 0.844661 ACCCTTCATGCACCCTACCA 60.845 55.000 0.00 0.00 0.00 3.25
3356 3486 0.394352 CACCCTTCATGCACCCTACC 60.394 60.000 0.00 0.00 0.00 3.18
3357 3487 1.032114 GCACCCTTCATGCACCCTAC 61.032 60.000 0.00 0.00 42.88 3.18
3358 3488 1.302949 GCACCCTTCATGCACCCTA 59.697 57.895 0.00 0.00 42.88 3.53
3359 3489 2.036256 GCACCCTTCATGCACCCT 59.964 61.111 0.00 0.00 42.88 4.34
3364 3494 1.022735 CTCTCATGCACCCTTCATGC 58.977 55.000 0.00 0.00 40.69 4.06
3365 3495 2.414994 ACTCTCATGCACCCTTCATG 57.585 50.000 0.00 0.00 41.87 3.07
3366 3496 4.574674 TTTACTCTCATGCACCCTTCAT 57.425 40.909 0.00 0.00 0.00 2.57
3367 3497 4.202461 ACTTTTACTCTCATGCACCCTTCA 60.202 41.667 0.00 0.00 0.00 3.02
3368 3498 4.327680 ACTTTTACTCTCATGCACCCTTC 58.672 43.478 0.00 0.00 0.00 3.46
3369 3499 4.373156 ACTTTTACTCTCATGCACCCTT 57.627 40.909 0.00 0.00 0.00 3.95
3370 3500 4.327680 GAACTTTTACTCTCATGCACCCT 58.672 43.478 0.00 0.00 0.00 4.34
3371 3501 3.440522 GGAACTTTTACTCTCATGCACCC 59.559 47.826 0.00 0.00 0.00 4.61
3372 3502 3.440522 GGGAACTTTTACTCTCATGCACC 59.559 47.826 0.00 0.00 0.00 5.01
3373 3503 4.327680 AGGGAACTTTTACTCTCATGCAC 58.672 43.478 0.00 0.00 37.44 4.57
3374 3504 4.640771 AGGGAACTTTTACTCTCATGCA 57.359 40.909 0.00 0.00 37.44 3.96
3389 3519 2.658807 AAGTGGGTCAAGAAGGGAAC 57.341 50.000 0.00 0.00 0.00 3.62
3390 3520 3.295973 CAAAAGTGGGTCAAGAAGGGAA 58.704 45.455 0.00 0.00 0.00 3.97
3391 3521 2.243736 ACAAAAGTGGGTCAAGAAGGGA 59.756 45.455 0.00 0.00 0.00 4.20
3392 3522 2.362077 CACAAAAGTGGGTCAAGAAGGG 59.638 50.000 0.00 0.00 0.00 3.95
3393 3523 3.023832 ACACAAAAGTGGGTCAAGAAGG 58.976 45.455 0.38 0.00 36.25 3.46
3394 3524 3.443681 ACACACAAAAGTGGGTCAAGAAG 59.556 43.478 0.00 0.00 40.34 2.85
3395 3525 3.426615 ACACACAAAAGTGGGTCAAGAA 58.573 40.909 0.00 0.00 40.34 2.52
3396 3526 3.080300 ACACACAAAAGTGGGTCAAGA 57.920 42.857 0.00 0.00 40.34 3.02
3397 3527 3.866883 AACACACAAAAGTGGGTCAAG 57.133 42.857 3.76 0.00 40.34 3.02
3398 3528 3.306364 CCAAACACACAAAAGTGGGTCAA 60.306 43.478 3.76 0.00 40.34 3.18
3399 3529 2.232452 CCAAACACACAAAAGTGGGTCA 59.768 45.455 3.76 0.00 40.34 4.02
3400 3530 2.232696 ACCAAACACACAAAAGTGGGTC 59.767 45.455 3.76 0.00 40.34 4.46
3401 3531 2.252714 ACCAAACACACAAAAGTGGGT 58.747 42.857 0.00 0.00 44.43 4.51
3402 3532 3.697045 TCTACCAAACACACAAAAGTGGG 59.303 43.478 0.00 0.00 43.72 4.61
3403 3533 4.398044 ACTCTACCAAACACACAAAAGTGG 59.602 41.667 0.38 0.00 43.72 4.00
3404 3534 5.106317 ACACTCTACCAAACACACAAAAGTG 60.106 40.000 0.00 0.00 44.93 3.16
3405 3535 5.007682 ACACTCTACCAAACACACAAAAGT 58.992 37.500 0.00 0.00 0.00 2.66
3406 3536 5.560966 ACACTCTACCAAACACACAAAAG 57.439 39.130 0.00 0.00 0.00 2.27
3407 3537 7.022055 CATACACTCTACCAAACACACAAAA 57.978 36.000 0.00 0.00 0.00 2.44
3408 3538 6.612247 CATACACTCTACCAAACACACAAA 57.388 37.500 0.00 0.00 0.00 2.83


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.